Doctor John
by HidingFromTheSpotlight
Summary: Everyone assumes Sherlock is the Doctor. He is brilliant after all. He seems like he's from another world, that he knows more than anyone could ever know. Well, they aren't entirely wrong. However, they are wrong about something crucial; Sherlock isn't the Doctor. And it hurts me to think that my friends don't recognise me, that they look straight through me like I'm nothing.
1. The Watch

**Another story I'm not planning on updating anytime soon! Sorry for being such a tease, but I couldn't help myself. Oh well, you know what to do.**

**Disclaimer: I do not own Sherlock or Doctor Who.**

**Doctor John**

_Everyone assumes Sherlock is the Doctor. He is brilliant after all. He seems like he's from another world, that he knows more than anyone could ever know. Well, they aren't entirely wrong. However, they are wrong about something crucial; Sherlock isn't the Doctor. And it hurts me to think that my friends don't recognise me, that they look straight through me like I'm nothing. I thought I was important to them. But obviously I'm not; otherwise they would recognise me, no matter how I look. I mean, even my 'arch-enemy' doesn't recognise me! If only River were still here… But she's not. She's dead. Dead and gone. Sherlock is the only one I can truly rely on now. He's the only one I can trust._

"Bored! Bored, bored, bored!" Sherlock yelled, throwing a pillow (of course it was John's) across the room. "John! Where's your gun?"

"Uh-uh, no. I am not giving you my gun so you can shoot the wall and drive Mrs Hudson up it." John replied, not lowering his newspaper.

"But I'm bored!"

"I don't care."

Sherlock let out an angry breath, flopping back onto the couch in a tangled, long-limbed mess. "What's wrong with criminals these days? Can't any of them use their imagination?"

"Perhaps they're afraid that the big, bad Mr Holmes will catch them." John mused.

"Oh please, John. You and I both know that most criminals are arrogant enough to assume they can best me, they just haven't the brains to come up with something interesting that has at least half-a-chance."

"Maybe if you're a good little boy, Santa'll bring you a nice serial killer for Christmas." John teased, finally lowering his newspaper. "Perhaps he'll reincarnate the 'Rhyming Reaper' for you."

Sherlock made a noise of disgust. "Really, John. I thought you would at least be above the use of such silly little names."

John shrugged. "It's easier to call him by a moniker than by his real name. I suppose it makes him less human and easier to tolerate."

"Why would making him less human make him easier to tolerate?"

"It makes what he's done seem a little less horrible. Or something like that."

"Ugh. People are so…"

"Human?" John offered.

"Yes. _Human_." Sherlock repeated derisively. "Sometimes I wonder how you can stand to be a part of it all; the _human_ race."

"I don't have much of a choice." John chuckled.

Sherlock frowned, looking at John in confusion. "Then why-" He cut himself off, sitting bolt upright as the doorbell cried out. "Client." He said automatically, practically leaping three feet in the air in his haste to get to his room. "Keep them busy for a moment while I get dressed!"

"You went to the palace in nothing but a bed sheet, yet you won't face a client without at least five minutes to fix your hair." John mused.

"If you'd care to actually time it, John, you'd find it only takes _two_ minutes." Sherlock replied. "And I do not 'fix my hair'. Would you really want me facing potential clients in my dressing gown?"

"I suppose you'd lose your air of professionalism."

"Exactly. Now, keep them busy for three minutes." Sherlock instructed, disappearing into his room.

John rolled his eyes and headed downstairs, meeting Mrs Hudson at the bottom. "It's a client." He told her.

She nodded, turning back to her apartment. "Alright, dear. Hopefully it will be something to occupy Sherlock's attention for longer than five seconds." She smiled.

John grinned in response, turning his attention back to the now frantically ringing doorbell. "Alright, alright, I'm coming." He called, opening the door. "Hi, I'm-"

"Is he here?" A red-headed female demanded in a heavy Scottish drawl.

"Sherlock? Yeah, he's here. If you go upstairs and wait he'll-"

The woman raced upstairs, obviously not listening to (or caring about) a word John said.

"-Be right with you." John finished awkwardly, glancing at the tawny-haired man who still hovered in the doorway. "Er, come in, Mr…?"

"Pond. Rory Pond. That was my wife Amy." The man said, offering John his hand and smiling tightly.

"Doctor John Watson. Nice to meet you. Sherlock's upstairs, so, if you'll follow me…" John trailed off, gesturing for Rory to follow him.

The two entered the flat to find Amy looking around, obviously searching for Sherlock.

"He'll be out in a moment. You can sit down on the sofa there and wait. Would you like some tea or coffee or something?" John offered.

"Tea?" Amy asked in disbelief, as though John had just insulter her mother. "You're offering _tea_ at a time like this? The whole world is in danger and you're offering _tea_!"

"Amy." Rory said softly.

John looked from one to the other, completely bewildered, then let it go. They were Sherlock's clients after all. "Right… Er, I'll just… go get Sherlock." He muttered.

"Good idea." Amy replied.

"No need, John. I'm here." Sherlock said, appearing in the doorway, in his usual high-end suit. "So, sit down, tell me about the case, but don't bore me." He warned, perching himself on his chair.

"I want you to look at this." Amy said, pulling out what looked like a broken fob watch and shoving it under Sherlock's nose.

Sherlock took it, turning it over in his hands, sniffing it and even licking it at one stage. He pulled a face and handed it back. "Ugh, Time Lord technology. Old. Gross."

"No, wait- you- you're supposed to open it." Amy told him.

"Only a Time Lord can open it." Sherlock replied.

"Duh, so open it and be a Time Lord again."

"Amy, I don't think…" Rory began.

"I'm not a Time Lord. I can't open it."

"You are and you can. You will." Amy insisted.

"Amy." Rory said again.

"What?" Amy snapped.

"I don't think it's him."

"But… the message. It said he'd be here. _Here_, Rory. Who else could it be?"

"Why don't you try asking _Doctor_ Watson?" Sherlock suggested.

The three of them turned to find John staring at the watch, completely entranced. Sherlock plucked the watch from Amy's grasp and lobbed it to John, who caught it with one hand. He stared at the watch, running his fingers along the cover. Memories rose to the surface. But… they weren't _his_ memories. At least, strictly speaking, they seemed like they weren't his memories. He frowned at the watch. "That woman… when I was a child, so very little, only seven… she appeared to me. She said she'd keep it safe for me… it was a gift from my Grandpa… and then… she told me to run." He whispered. "Goodbye… my love. She… yelled it to me, and when I… glanced over my shoulder… she was gone. And I… the nightmares stopped. After she took it. But… when I went to… Afghanistan, they- they started again. Then, when I met Sherlock… the nightmares stopped… and I dreamed. I dreamed of stars… of worlds so very far away. Of places I could never know, yet I dreamed of them. And- and the people I dreamed of… so many friends… so many enemies. So- so many… dead."

"Open the watch, John." Sherlock urged. "Open the watch and you'll understand."

John did as he was told. And then his life changed, completely.


	2. Doctor John

**So, here's another chapter. I just want you all to know, I have absolutely no idea what I'm doing. Also, I have no beta, so if you see something that doesn't make sense or I've misspelled something, do let me know. Anyway, enjoy!**

**Disclaimer: I own neither Doctor Who or Sherlock. **

**Chapter Two:**

**Aproximately Thirty-Seven Years Ago:**

"Honey? Was that the door?" Mrs Watson called, setting a pan on the stove.

"Yes, dear. I'll get it." Mr Watson called back, walking towards the door as it rang more insistently. "Yes, I'm coming. Keep your knickers on." He pulled the door open. "Hello, I'm-"

"Help. Please, t- take him. Keep him safe." The woman gasped, holding out a bundle of cloth. "Help. Please. J- just take him. Please."

Mr Watson accepted the bundle, holding it close to his chest. "Are- are you alright? Do you, um, need me to call you ambulance? Come inside, please. I'm- I'm a doctor, I can help."

The woman smiled briefly. "No, but… please. Keep him safe."

"Is there anything I can do? For you?"

The woman paused and then reached into her pocket and pulled out an ordinary silver fob watch. She handed it to Mr Watson, and turned away. "Keep that with him, but don't let him open it. And please, keep him safe."

Mr Watson looked up, halfway through another in an endless line of questions, only to have it die as he stared out his front yard. The woman was gone. He looked down at the bundle in his arms, peeling back the lip to find an infant, maybe one or two years old. A little boy, still sleeping.

"Honey? Who is it?" Mrs Watson asked, walking towards the door.

Mr Watson turned around, still slightly flabbergasted by the way things had happened so suddenly. "I think we just adopted a baby."

John Watson, or rather, the Doctor, stumbled back, still reeling at the information being unlocked within his mind. Memories, so very many memories, unleashed themselves upon him, stabbing him with sorrow and loss. But then other memories rose, forming a shield against all the pain. He let out a gasp as the last of his memories, the ones from directly before he regenerated, slid into place. The Silence had been plotting something, something big. He and River had been on the verge of discovering exactly what that was when… disaster. The details were still fuzzy, but he was sure that he got hit with some sort… something. And then River held back the rampaging thingywhatsits while he regenerated and then… well, he couldn't really see anything after that, but he could have sworn someone yelled something in some sort of gobbledygook and then he was being carried and then he must have fallen asleep because his memories beyond that are just of growing up. Mr and Mrs Watson, and then Harry. His first crush, his first kiss, his first girlfriend, so many firsts. And then there was Afghanistan. Sun and sand and blood, screams and yells and gunfire, pain ripping through his shoulder. Back to England, crippled, already missing the thrum of adrenaline through his veins. Sherlock, strange and wonderful and so very different, fighting a battle of his own, a battle against the boredom of everyday life.

"Doctor?" Amy whispered, shuffling over to him.

"Stay away." The Doctor croaked, leaning against the wall for support.

"But Doctor, I-"

"Stay away from me!"

"Out." Sherlock ordered. "Get out, both of you."

"But we're-" Amy began, looking aghast at the demand.

"Out." Sherlock repeated, and with a violent shove he pushed Amy and Rory out the door. Amy beat on the locked door with desperation, but Sherlock ignored her as he pushed John's armchair up against the door. Turning around, Sherlock observed John/the Doctor. "John?"

No response.

"Doctor?"

Still no response.

Sherlock frowned. Folding his arms across his chest, he slumped down into the armchair not currently pressed against the door and waited. This lasted for five minutes, then Sherlock let out a sigh and pulled himself to his feet. "Look, how long is this going to take? Because right now, I'm bored."

The Doctor let out a broken laugh, glancing up at his… at Sherlock. "I'm sorry if my little identity crisis disinterests you."

"What identity crisis? You're John, and apparently you're this Doctor. Doctor John Watson."

"I also happen to be a Time Lord, despite the fact I've spent the last thirty-seven years of my life believing I'm human. Believing that I was just an ordinary, everyday human being."

Sherlock shrugged. "Isn't this better, then? Being a Time Lord rather than a human sounds much more interesting, Doctor John."

"It's just the Doctor."

"No. You're Doctor John. That's how I've known you, and that's how you'll stay."

Doctor John smiled. But then something occurred to him. "Wait… How do you know about Time Lords? You knew about my watch just by licking it."

Sherlock grinned, dropping into a crouch. "What do you think, Doctor John?"

Doctor John's eyes widened. "You've got to be kidding."

Sherlock tilted his head, still smiling. "I'll give you two guesses. It's obvious really."

Doctor John frowned, crawling closer. "This would be easier if I had my screwdriver." He muttered, his nose an inch from Sherlock's. A smirk scrawled its way across his face has an idea burst forth and he acted before he could fully think it over.

Sherlock barely had time to let out a curious (startled) "Hmm?" before Doctor John's lips were crushed against his own. His eyes bugged out, registering that (Doctor) John 'I'm-not-gay' Watson was _kissing_ him.

Doctor John pulled back, a thoughtful expression playing across his face before it was replaced by a grin. "Ah, Anthromechanocyte."

"And you got all of that just from a kiss. I'm impressed."

Doctor John just shrugged. "So, what's an Anthromechanocyte doing on earth? Particularly in the 21st century."

"My people were experimenting with time travel. Mycroft and I were the head scientists, and we volunteered to be the test subjects. But… it didn't work quite as we planned. It seems we could only go one way. We ended up here. Mycroft took a liking to your government and managed to gather together enough documents for us to pass as two ordinary brothers. It's laughable to think he now runs the government."

"Aliens in Downing Street. To think that was once a bad thing."

"Yes, I heard about that. Was that you who chased them all away?"

"Uh, sort of. It wasn't me, me, it was one of the other me's. I mean-"

"I'm familiar with the Time Lord lifecycle, Doctor John."

"Oh, okay. So, is Sherlock your real name?"

"No but I prefer it. You would too if your birth name was Kappa-Beta-Twenty-Two-Twenty- Het."

"It isn't that bad. A bit long, maybe, but not that bad." John sat back. "Well, this certainly explains why you barely ever eat or sleep. But how did you power your other half?"

"Mycroft, for lack of a better word, plundered a few alien research labs in order to salvage any sort of technology he could find."

"Is he your double?"

"Yes."

Doctor John was silent for a moment, running his fingers through the veritable ocean of memories that now resided inside his mind. "So, what now?"

"What do you mean?"

"Well, I have to find my TARDIS and figure out what's going on with the Silence. Are you going to come with me?"

"Do you want me to?"

Doctor John smiled. "Of course. You showed me your battleground, I might as well show you mine."

"What about the other two? The girl and boy?"

Doctor John bit his lip. "Well, they did come all the way here to find me, even if they were looking in slightly the wrong place."


	3. Dude, Where's My TARDIS?

**Hello! Sorry, it's been awhile since I posted. Anyway, here you go!**

**Disclaimer: I do not own Sherlock or Doctor Who. They belong to their respective creators. **

Chapter Three:

"What makes you so sure the TARDIS is here?" Rory queries as he, Amy and Sherlock followed the Doctor through the mildly crowded London streets.

"If I or my TARDIS is in danger it automatically begins a shutdown sequence. I programmed the TARDIS to transport itself to a safe place. This is the safe place." Doctor John replied, rounding a corner.

"I highly doubt a street in Lo- Oof." Sherlock was cut off as he collided with the back of Doctor John.

"It's gone." Doctor John said with a frown, staring at an area of wall on the opposite side of the street.

"As I was saying." Sherlock murmured, hands in his pockets. "Leaving anything in a street such as this is never a good idea. There are at least seven people walking past us right now who have a record of various crimes such as burglary, breaking and entering, and all the other boring crimes. Any one of them could have seen your TARDIS and stolen it. I mean it has been here for… how many years?"

"Er, thirty-ish. But it can't have been stolen. You can't just _steal_ the TARDIS. If you don't know it's the TARDIS, you don't notice it."

"Good thing we had someone who knew what it was then." A familiar, posh voice said.

The group spun around in surprise.

"Mycroft!" Sherlock snapped, striding towards his brother. "What are you doing here?"

Mycroft raised an eyebrow. "Is that really the correct way to greet your brother?"

"Double." Sherlock shot back.

"Brother."

"What have you done with my TARDIS?" Doctor John demanded, striding forwards and glaring at Mycroft, which would have been more impressive if it weren't for the dramatic height difference.

"_I_ did nothing. One of my associates, however, moved it. If you'd follow me, I can take you to it."

"Why don't you bring it here?"

"Because there's something I need to show you as well, and it isn't what one would call 'mobile'. So, will you come? Or do I have to drag you there?"

"I'd like to see you try that." Doctor John scoffed.

"You and I both know it can happen, Doctor. If only because you're curious."

"Who says I'm curious?"

Mycroft smirked, turning on his heel and marching away. Doctor John hesitated half a second before following throwing a casual, "Come along Ponds, Sherlock," over his shoulder as he went.

Sherlock made a noise, catching up to John in two strides. "Do we really have to follow him? How do we know he isn't leading us to our death?"

"I thought you two were brothers." Rory frowned.

"So were Scar and Mufasa." Sherlock said dismissively.

"I am not leading you to your deaths, I assure you." Mycroft replied.

Doctor John, however, was more interested in Sherlock's statement. "Since when do you make pop culture references?"

Sherlock rolled his eyes. "Since I watched the Lion King with you in hospital."

"Oh right, I nearly forgot about that. I love the Lion King. I once quoted it to the Sycorax."

"The what-er-rax?" Amy asked.

"Sycorax. Long story, maybe another time." Doctor John replied, suddenly jogging to catch up to Mycroft. "So, Mycroft, if that's your real name-"

"It's not. My real name is Kappa-Alpha-Twenty-Two-Twenty- Het. But that is rather a mouthful, not to mention I dislike it." Mycroft answered.

"Right. So, Mycroft, where are we going?"

"You'll see."

"I wasn't really asking."

"I know." Mycroft smirked.

After a few minutes of walking, they came to a rather unimpressive building, but rather than walking through the front doors, Mycroft led them down a side alley to a dingy, rusting emergency exit.

"We can't go through here, they only open one way." Rory said, beginning to turn around.

Mycroft pressed a brick to the right of the door.

"Please state your name and access code." A disembodied female said.

"Mycroft Holmes, 4734."

"You are surrounded by unverified individuals; please state their names and species."

"Amelia Williams, human, Rory Williams, human, Sherlock Holmes, Anthromechanocyte, and the Doctor, Time Lord."

"Names and species noted. Verifying, please wait."

Mycroft let out an impatient breath, muttering something about, '_primitive earth technology_'.

"This place seems familiar." Doctor John murmured.

"Does it?" Mycroft queried, only half-interested.

"Names and species verified. Opening doorway."

"Good." Mycroft murmured stepping back. "After y-"

The entire wall, emergency exit included, slid sideways, but before anyone could move, a figure leapt out at them, gleefully yelling, "Doctor!"

Doctor John had barely a second to register who it was before he found himself flat on his back with the figure squeezing him round the middle like a half-empty tube of toothpaste. After a moment of struggling, John managed to push the man back, gasping.

"Hi, Doctor." The man beamed.

"Hello Jack." John groaned, massaging his stomach.

"Doctor? Who's this?" Amy asked.

Jack shot to his feet, smile widening. "The name's Captain Jack Harkness, but you can call me Jack. You must be the Doctor's companion." He said, offering his hand to her.

Amy glanced to Doctor John, before she accepted the proffered hand and shook it. "I'm Amy and this is my husband Rory." She said, indicating Rory with a wave of her hand.

"A pleasure to meet you, Rory." Jack shook his hand as well before glancing around and spotting Sherlock. "Ooh, who's this, Doctor?"

"Down, Harkness. You're still working." Mycroft said, tapping his umbrella impatiently.

"As you say, Mr Holmes." Jack replied, saluting. "After you, _sir_."

Mycroft raised his eyebrow at Jack, then took the lead. Jack grinned at the other four, beckoning for them to follow him inside.

"So, Doctor, what have you been doing since I last saw you? New face, eh?" Jack asked, strolling along beside Doctor John. "Not to mention you're a lot shorter."

Doctor John rolled his eyes. "I'm actually on my twelfth regeneration. The one before was a bit younger. Loved bow ties, fezzes, that sort of thing. Got married to a very lovely woman, River Song, though her name is Melody Pond, their daughter." He indicated Amy and Rory with a jerk of his head. "Long story short, she had Time Lord-ish DNA because she was conceived in the TARDIS mid-flight and was kidnapped by these alien things that, when you look away from them, you can't remember them, but that didn't work out that well, she married me after all."

"Sounds like quite a busy life." Jack laughed.

"Speaking of Melody, where is she?" Amy queried.

Doctor John froze.

"Doctor?" Rory said suspiciously.

"You have to understand… there was nothing I could do." Doctor John replied in a low voice.

Rory's eyes blazed as he stepped forward. "What. Happened. To. Melody." It wasn't a question the Doctor could weasel his way out of. It demanded an answer, one that would break his heart and most definitely theirs.

Doctor John took a deep breath, preparing for the worst.


	4. Hey, Sexy

**Decided to tease you all again with a short chapter. I have a feeling this story's gonna be really short (or at least, you know, six chapters minimum) and I figured out a major plot twist! But I won't tell you til later. So, please tell me what you think. And I don't mind corrections where corrections are needed :)**

**Disclaimer: I do not own Doctor Who or Sherlock.**

Chapter Four:

Doctor John watched as Amy and Rory disappeared around the corner, hand pressed to his cheek. Behind him, Jack coughed awkwardly and Mycroft tapped his umbrella against the ground. Sherlock stepped forward, peering at the Time Lord with as much concern as an Anthromechanocyte could possibly muster. "Are you alright?" He whispered.

"Yeah. I'm… used to it." Doctor John muttered, turning away from where the Ponds had disappeared. "Anyway… you were taking me to my TARDIS."

"You don't want to go after them, Doc?" Jack queried with a frown.

"I just told them that their only daughter is dead. I doubt they want to see me right now."

"Okay, Doc. This way." Jack gestured to a door, which slid open at his touch. "So, Doctor, where've you been all this time? And why'd you leave the TARDIS just lying around?"

"I didn't just leave her lying around! I had her parked quite specifically. _You_ moved her." Doctor John replied.

"I did it for her safety." Jack retorted, opening another door and standing back. "She's in there, Doc. Go say hello."

John rushed through the door, heart banging against his chest. He couldn't help it if he was grinning like a five-year-old who had rediscovered their favourite toy, and he certainly couldn't help the spring in his step as he skipped towards his beloved blue box. "Hello, old girl! Did you miss me? I sure as hell missed you. Well, I've missed you for as long as I've been a Time Lord again. But never mind, because we're together again!" He declared, throwing his arms around what parts of her he could reach. Later, he would swear he felt a joyful hum in response to his touch.

"So… this is your spaceship?" Sherlock queried, stepping into the room and running his eyes over the TARDIS in a way that was almost indecent.

"She's my TARDIS. And I'm her Time Lord." Doctor John answered.

Sherlock raised an eyebrow. "_Her_ Time Lord?"

"Yes. She stole me, and I her."

"You never told me that story before." Jack muttered, sidling up to John's other side.

"That's because I only ever heard her side of the story _after_ you had gone. Or, I had gone. The other me, I mean." Doctor John jumped back with sudden vigour, clapping his hands together. "But enough of that. Let's get inside, people to do, things to see!" He exclaimed excitedly, then paused as his brain caught up with his mouth. "Wait, stop, reverse that. _Things_ to do, _people_ to see."

Jack snickered in a manner that was most certainly _not_ fitting for an adult.

"Captain, please try to maintain a shred of maturity." Mycroft said with disdain, rolling his eyes. "You still, however much you may dislike it, work for the government and we must preserve a certain image of authority and dignity."

Jack grinned. "As you say, _Sir_."

"Jack, stop it." Doctor John told him sternly, opening the door of the TARDIS and stepping inside.

"Stop what?" Jack asked innocently.

"Stop flirting."

Jack huffed and strode in after the Doctor. "I wasn't flirting. I would _never _flirt with a superior. It would be inappropriate." He added, looking scandalized.

Doctor John laughed. "Right, sorry. I must have been _mistaking_ you for someone else." Glancing to the door, he noted that Sherlock and Mycroft were still hovering outside. "You can come in, you know."

"We're waiting for permission." Mycroft said.

"I just gave it."

"Not from you." Sherlock said, looking up.

The TARDIS hummed and shuddered, the console glowing pleasantly. A few of the loose wires sparked. Mycroft and Sherlock stepped inside, ducking their head to the console. Both Jack and Doctor John frowned.

"Er… are you two _bowing_ to my TARDIS?"

"We were raised to have manners when in the presence of a superior being." Mycroft replied.

"All right then." Doctor John turned back to the console and started to pull up various readouts and images on his monitors. "Hmm, we'll have to take it to Cardiff so it can absorb a few more Huon particles." He said absently.

"What about this… Silence?" Sherlock asked.

"That's in the future. All I have to do is key in the coordinates and we'll be there after I left."

"What about Amy and Rory?" Jack queried.

Doctor John was quiet for a moment, pretending to straighten something. "I doubt they'd want to come with me… be near me. After all, I'm the reason their daughter is dead." He said in a whisper.

"Doctor, you must really be dense if you think we'd wait all this time to just let you get away from us." Amy declared, walking into the TARDIS, husband in tow. "Granted, when this is all over I'm going to beat your backside black-and-blue, but my daughter was willing to, and did, die for you, so you must be bloody well worth it."

"Amy." John said, a slow smiling spreading across his face. "Rory."

"I'd like to point out that I'm still mad at you… but you're also my friend. And I know that everything you do, is to help people. That's- That's what I want to do. So… I- We- We're willing to- to push away our grief, to put it in a little box until this all over, and do what needs to be done." Rory said quietly.

"Right, then. Let's get going." John replied, grabbing a lever and pulling it down sharply. As the TARDIS rumbled and groaned, jolting its passengers, Doctor John couldn't help but grin, because his two worlds were not just colliding, they were melding together.


	5. Well, We're Screwed

_A/N: Hello, I'm back with another chapter for you all! I'll save the overlong note for the end, but I will say this: YOU'LL BE SURPRISED (hopefully)._

**Disclaimer: I do not own Doctor Who or Sherlock.**

**Chapter Five:**

Immediately upon landing, Doctor John marched out of the TARDIS, the others following closely behind. He crept to a corner and peered round it, eyes scanning the area with ease. Satisfied that no one had overheard their landing, he turned back to his gaggle, grinning excitedly. "Right then, we're in the depths of the Silence's base, completely outnumbered, with no idea why we're here. Isn't it exciting?"

"Sounds fun." Jack grinned back. "Anything planned?"

"Er, let's avoid dying and/or destroying any planets." Doctor John said.

"Noted. Should we stay as one large group and risk getting captured or split up and have a greater chance of succeeding?" Sherlock suggested.

"We'll split up, have a poke around and return to the TARDIS before anything goes wrong. Hopefully." Doctor John clapped his hands together lightly. "Right, shall we send the married couple off first? Then I think Jack and Mycroft will work well together-"

"What reasoning are you basing that inference on, John?" Mycroft asked, raising an eyebrow at the Time Lord.

"Sound reasoning, I assure you." Doctor John replied.

Mycroft rolled his eyes and turned away, heading down a hallway to the left, calling, "This way, Captain Harkness."

Jack winked at Doctor John. "Later, Doctor."

Doctor John turned to Sherlock. "Shall we go see what mysteries we can find… and maybe poke with a stick?" He grinned, gesturing to the darkest of the passages.

"I never thought you would be the one to suggest we go looking for trouble." Sherlock murmured.

Doctor John shrugged. "I'm the Doctor, I always go looking for trouble."

"John, these aliens we're after, what do they look like?"

"Ah… I'm not entirely sure. You see, the minute you look away, you forget everything about them. There's really no way to stop it. But I'll know them when I see them." Doctor John replied.

"John, stop." Sherlock commanded.

John paused and turned around, finding Sherlock had stopped a few feet behind him and was staring down one of the passageways. "What is it?"

"I'm not sure." Sherlock said slowly.

"I'm sure it's harml-" Doctor John froze. And for the second time today, he remembered so many things he didn't know he had forgotten that it really wasn't funny. "Do you have a pen on you, Sherlock?"

"No, why do you ask?"

"We need to mark down that we've seen it, keep a tally." Doctor John explained, patting his pockets without looking away.

"That won't be necessary, John. Why don't you follow me and I'll let you know exactly how many there are." A voiced cooed.

Sherlock spun around, his face going blank for a moment before contorting back to an expression of rage. "You!"

"Not now, Sherlock." Moriarty said airily. "Daddy's busy playing with the big boys."

"I take it it's you then." Doctor John said calmly.

"Say my name, Doctor."

"Master."

Moriarty grinned. "It's certainly been a very long time, hasn't it?"

"John, he's a Time Lord too, isn't he?" Sherlock asked, still glaring at Moriarty.

"Yeah. We go way back… I thought you were dead, Master. Properly dead, I mean."

"You know me better than that, Doctor. I did it once, what could stop me from doing it again? And please, call me Moriarty. It is known to the people of Earth, and it frightens them. Even after I did my best to destroy it, it is still there, in the very back of their memories."

"They barely remember you." Sherlock hissed.

Moriarty grinned. "Exactly. They think I am dead, but in their heart of hearts, they know I will never be gone."

"So… you've taken control of the silence, have you? Or do you serve them?" Doctor John asked, his light and innocent, almost joyful.

Moriarty's face twisted as if doused in pure lemon juice. "I serve no one! I am their leader! And I will lead them to their greatest victory; your demise." He snarled.

"Will you?" Doctor John replied. "Would you really see me destroyed?"

"Yes!" Moriarty cried, an insane laugh tumbling from his lips.

"Then _you_ will be the last of the Time Lords, and I will be able to rest." Doctor John said quietly.

"John?" Sherlock whispered warily.

"Grab them! Take them to the centre!" Moriarty shouted. "And there, we shall see them executed!"

"You have a plan, don't you?" Sherlock asked, voice barely above a whisper.

"As I said before, my plan is to avoid dying. And to accomplish what I first set out to do." Doctor John said, raising his hands in surrender. "Just do as I do, Sherlock. We'll be fine."

And so, they were marched through the lair of the silence, Doctor John making sure one of the Silence was always in his sight, and Sherlock studying everything he could about their surroundings. Moriarty trailed behind them, whispering threats and sick jokes in their ears. Sherlock ignored him for the most part, though there was a moment where he looked as though he might turn around and strangle Moriarty after he made an obscene comment about their "wisp of a housekeeper" and what he'd do to her when he got back to earth.

Soon, however, they came to a large, open space, teeming with the Silence and other aliens just as strange and fascinating, and all just as pissed at the Doctor. Moriarty moved to the front of the group, arms held aloft. "I told you I'd get him." He called to the crowd. "Here he is, the Oncoming Storm, the Predator of the Daleks, the one, the only, Doctor!"

The crowd murmured in response, peering at him with curiosity and hatred. A few people jeered. Doctor John and Sherlock were lead to a holding ring next to the stage, where Amy, Rory, Mycroft and Jack stood, watched over by fierce guards. Amy looked furious and blood was spilling from Rory's split lip. Mycroft looked mildly ruffled, and only a little bit peevish, as though this was merely a minor negation gone slightly wrong. Jack was the only one who seemed cheerful, smiling and waving at the crowd like a movie star.

"Doctor!" Amy called, racing forwards as Doctor John and Sherlock were pushed inside. "What's going on?"

"They're going to execute us." Sherlock replied. "And very crudely, I might add." He said, nodding to the stage where a wooden chopping block could be seen.

Moriarty climbed onto the stage and the crowd fell silent. Tucking his hands behind his back, he smiled wolfishly at them. "So, the day is finally here. Today is the day we destroy the menace that is the Doctor. And it will certainly be a sight to see. Of course, some of you were worried that the Doctor, being a Time Lord like myself, might regenerate the minute we bring the axe down on his neck, but never fear, I have a way of counteracting that, which I will demonstrate shortly. Now, how about we cut to the chase? Bring out the Doctor!"

The crowd cheered as Doctor John was dragged out of the pen and across to the stage. Moriarty grinned, stepping towards him. "Any last words, Doctor?"

"You won't win, Master. You never do." Doctor John replied.

"Oh, I think I will this time." Moriarty grinned. Gesturing to the escorts, Doctor John was pushed forward once more, forced to kneel in front of the block. The executioner took his position, raising the axe high above his head. The crowd got to its feet, holding a collective breath. Across the room, Doctor John could hear Amy challenging various guards to take her on, swearing to destroy every one of them if they hurt her friend. Doctor John smiled and turned towards the sound of her voice. At least, if he were to die, the last thing he heard and saw would be his friends.

Just as the axe was about to make its downward swing, a cry was heard across the chamber, causing the rooms inhabitants to all swivel in alarm: "That isn't the Doctor!" Throwing back the hood of his cloak, hair gleaming, bow tie proudly on display, the Eleventh Doctor stood tall, fixing Moriarty with a serious and disapproving look. "I am."

**A/N: So, are you surprised? I hope you are. And I bet there was a moment of "oh that's not very surprising" and then "Wait, what?" I hope there was. But anyway, tell me what you thought. I'd love to hear from you!**


	6. Before You Ask, Yes I'm Very Evil

**A/N: If there is a grammar or spelling mistake or a plot error please point it out to me because I literally finished this like five minutes ago and I have felt so bad because I've barely been updating any of my stories. Also, I regret nothing. There is only one chapter after this and it will be the epilogue which will hopefully wrap everything up nicely.**

Chapter Six:

The sudden murmuring and shouting and cries of disbelief were almost deafening. John's mouth was hanging open and Moriarty wasn't much better. He recovered quickly, though, going from shock to anger. Amy and Rory seemed to be too shocked to register the Doctor's (_their_ Doctor) appearance. Sherlock and Mycroft seemed to expect it, and Jack was just as unsurprised. The Doctor strolled further into the chamber, smiling and waving cheekily to the outraged viewers. "I know many of you came here expecting to see me die. Well, I'm sorry but there's been a change to the program. I'm not dying today, I have other plans. So, if you don't mind, I'll be taking my friends and leaving."

"You think you can just walk in here and take over, Doctor?" Moriarty thundered.

"No, but I can walk in here and walk out with more people than I did." The Doctor replied cheerily, gesturing to Amy and Rory. "Come along, Ponds, it's time to go. And bring your new friends too. Jack! How have you been?" He exclaimed.

Jack beamed, jumping the barrier and strolling to the Doctor's side. "Well, Doctor, you're looking young."

"Oi!" John yelled, indignant despite himself.

The Doctor's head snapped towards where John knelt, head still resting on the chopping block. A dark cloud settled over him, eyes flashing in anger. "Let him go." He ordered.

Moriarty quirked an eyebrow. "So you have a soft spot for this one, eh?" He smirked.

"I won't say it again." The Doctor said. He stepped forwards, pulling his screwdriver from the folds of his robes.

"What are you going to do? Build a cabinet?" Moriarty sneered.

"How rude." The Doctor snapped, he pointed it towards the ceiling. It screeched and Moriarty laughed, thinking it a diversion. It wasn't until the air vent above him collapsed on top of him that he realised what the Doctor had planned. "Run!" The Doctor yelled, brandishing the screwdriver at the crowd.

John wouldn't have run, despite the order, because his brain was still stuttering and stammering over the fact that his eleventh regeneration was _here_, potentially endangering everyone, and had said he wasn't the Doctor. Neck deep in frantic thoughts, he didn't notice Sherlock carrying him out of the arena as fast as his long legs could carry him. Behind them the crowd was in uproar, shouting and screaming and falling into a chaotic dance of death and destruction. The Doctor ran, gripping onto Amy and Rory, followed by Jack and Mycroft. Moriarty let out a howl of pain and frustration.

"Follow me!" The Doctor called, overtaking Sherlock. He ducked down a few hallways, weaving this way and that at a dizzying speed. He sped into an empty room and slammed the door as the last of the group made it inside.

"Right, so we're going to need a plan-"

"WHAT THE HELL IS GOING ON?" John bellowed, scrambling off Sherlock's shoulders.

"Look, shush, it's okay, just let me-" The Doctor began, reaching for John's shoulder.

"WHY DID YOU SAY I WASN'T THE DOCTOR?" John yelled, eyes starting to water. "I AM THE DOCTOR! I AM! ALL OF THESE MEMORIES- WHAT ELSE COULD I BE?"

"My son." The Doctor murmured. "You're my son."

John gaped at him, nearly choking as a thousand questions tried to flood out at once. "Wha- No- How- I can't- What?"

"I know this is difficult to understand, but you have to believe me, John. You're my son. And… River is your mother." The Doctor said, gripping John's elbow.

"What? But I- But the watch, it-"

"The watch- The watch was a ploy. A diversion to make everyone believe I had regenerated. I- I'm sorry, John. I'm so sorry."

"You say that. You've said that so much. So why does this keep happening? How many people have died, died for you, and all you could do was apologise?" John growled, pushing the Doctor away.

"John, I-"

"DON'T MOTHERFUCKING JOHN ME! YOU HAVE YOU'RE FRIENDS TIP OVER MY ENTIRE WORLD AND MAKE ME THINK I'M YOU! YOU MAKE ME TAKE ON GUILT THAT WEIGHS MORE THAN A MILLION FUCKING PLANETS! ALL SO YOU CAN FAKE YOUR DEATH AND BRING DOWN THE SILENCE? SO YOU CAN DESTROY THE MASTER ONCE AND FOR ALL?" John yelled.

"John." Sherlock whispered. "Stop. Calm down."

"I AM COMPLETELY CALM!"

"John, if you're going to yell at him, you may as well yell at me. I was a part of this." Sherlock snapped.

John gaped at him. "What? No. No, you- you can't-"

"Exactly one month before we met, the Doctor came to me and told me that I would soon come upon something very rare: the child of a Time Lord and a human. But I wouldn't be allowed to tell him what he was. I could, however, associate with him, so long as I didn't reveal who I was. Then he told me that someone would come looking for this man, and they would assume it was me, I was to make sure they were directed to him." Sherlock explained quietly.

"So you- when we met, you'd already-"

"No. My deductive abilities are not a trick, John. You should know this by now." Sherlock said impatiently. "Now, could you please put off your identity crisis until _after_ we've gotten away?"

John glared. "Fine, but when this is done, I'm kicking your ass from here to Saturn."

"Doc- Doctor?" Amy finally said, stepping forwards and prodding him.

"Ow! Gentle, Pond!" The Doctor whined.

"You idiot! You made me think you were dead, _again_?" Amy shrieked, whacking him across the arm and then again on the back of the head and on his shoulder and again and again until she was a flurry of fists pummelling into every inch of the Doctor she could reach, along with a great deal of angry/sad crying and swearing.

"Ow! Rory! Rory make her stop!"

Rory inclined his head to the side, considering it. "Sorry, Doctor, but I don't think I want to get near her when she's this angry. Might become a casualty, you know."

"Rory that's not helpful!"

"Neither was you faking you're death so I guess we're even." Rory replied, folding his arms over his chest.

"Rory, please! I had to!"

"Although this is entertaining, I think it would be best if we moved on to getting away from the enemies who wish to kill us. Further away if possible." Mycroft said drily.

"I guess you're right." Amy said petulantly, giving the Doctor one last slap on his shoulder. "So, where's the exit?"

The Doctor grinned (after dusting himself off and straightening his bow tie) and tapped one of the wall panels. The panel slid away with a quiet hiss, revealing the room they had originally landed in. There was a sudden pounding on the door, which everyone knew meant that their enemy had found them. The group hurried into the TARDIS room, bar one. Pressing the panel the Doctor had used to open the door, Mycroft smiled bitterly as it closed. There was a pause as his wavelengths registered to his double, who was immediately rapping on the wall in an attempt to open it again.

"Mycroft? Mycroft, what are you doing?" Sherlock called.

"Just ensuring our victory, Sherlock, nothing to worry about." Mycroft replied, running his fingers over a cannibalised piece of computer equipment (more than likely the work of the Doctor in an attempt to sabotage his enemies). Within a few minutes under his expert hands, the machine came to life, humming appreciatively. "Now, let's see what we can do, eh?"

"Mycroft, what are you doing?" The Doctor called. "What have you done to this door?"

"I've locked it, Doctor. I would have thought that obvious." Mycroft answered, removing the flesh-like glove which covered his mechanical hand. He flexed it and watched as wires began to snake out of his fingertips, implanting themselves into the machine. With his free hand, he summoned a chat window into the next room. Looking up, he found the others staring at him in various degrees of surprise.

"What are you doing?" John demanded.

"Buying you some time. Now hurry into the TARDIS; I'll be right behind you." Mycroft said, twiddling a lever on the machine. Warnings flashed before his eyes, literally. His connection with the machine, with every single technological device on this station, tightened and he realised his previous statement had been wrong. He didn't correct it.

"Mycroft." Sherlock said, and when Mycroft looked up, he found his double saluting him in their home planet's traditional custom. Considering his double had hated, and loudly complained about, tradition and other such niceties, Mycroft found himself feeling rather touched. In seconds, Sherlock had fallen back into his rigid, unemotional posture. And the moment was over. Mycroft closed the window and Sherlock turned on his heel and marched into the TARDIS. One by one, the others followed him. There was a look of quiet anger in the Doctor's eyes as he gazed one last time at that stretch of wall, before he closed the doors of the TARDIS in a resigned silence.

Inside, only the soft screeching of the TARDIS as it powered up was heard. The Doctor gripped the railing until his knuckles whitened because this would be another life lost because of him. More guilt, more pain, more sadness to tear at his already fractured soul. He was tired and hurt and _why wouldn't the memories stop_? Why did their faces keep flashing in and out of focus? Why could he never get one night without the nightmares and names of the long dead and the recently dead and the not quite dead yet on his lips? Why were there always more?

The TARDIS landed with a thump in London, not far from a particular flat, but the occupants barely noticed, too preoccupied with their heavy hearts. John was pressed against the wall, trying to suppress the memories of sun and sand and blood. Gunfire rattled off in his eardrums. Screaming and shouting as comrades and civilians and enemies were mowed down and blown up. And then the memories that weren't his, that belonged to a man standing less than six feet away, started ripping through his mind. The pain tore through, the memories like spikes of ice. Freezing and melting and freezing and melting and he couldn't take this and what was that in his hand.

"Alright, John?" Sherlock murmured, tightening his grip on John's fingers.

"I'm fine."

"Are you sure?"

"Since when are you ever concerned about my emotional well-being?" John muttered.

"Since I decided I did." Sherlock answered back. "Now, what shall we do now?"

"Perhaps I was a little too hard on him." John said softly, staring at the Doctor as he paced the console room. "Maybe… Do you think I should stay with him? He is my dad after all."

"I don't know about all this '_I_' business, but _we_ will certainly be going on many, many adventures with the Doctor." Sherlock said with a slight smirk. "As long as they're not boring, of course."


	7. Epilogue

**A/N: So this chapter is just tacked on at the end to quickly illustrate that River's not dead.**

Epilogue:

John lay awake in his bed aboard the TARDIS (a bunk bed because his father had insisted) thinking of how different his life had become, without changing at all. He had gone from a damaged soldier with no war to fight to the sidekick of a consulting detective on the battleground of London to the most dangerous man and yet the kindest in existence to one of many travelling the stars. He had left behind sun and sand and blood and gunfire, noise and bustle and streets filled with strangers and mystery, and traded it all for stars and planets far away and love. And yet he hadn't. He could still find noise and strangers and mystery, there was still sun and sand and blood, all while running with the Doctor.

Although his father had removed the thoughts that weren't really his, John still felt their ghosts. He still knew that every second of every day was filled with loss and pain and _remembering_ everything. All the friends he had lost and loved and known. The family he would never hold again. The countless enemies he had fought, and had _killed_, in an attempt at peace. The civilians who had done nothing more than be in the wrong place at the wrong time, who had simply been in the way, who had died because they existed. And most of all, all the people he couldn't save. The people who wouldn't let him save them. Those people who had sacrificed for him, for the ones they loved, for the world. The faces that haunted him at every turn, that never tightened their grip on his hearts. John knew how much his father suffered their fates, how he relived their last moments in the quiet and the calm, in those moments when there was no more noise, no more distractions. How, without anyone to keep his attention, the demons came screaming up his spine and gnawed at his heart and dug their claws into his brain. The screams that filled his ears until he wasn't sure if they were memories or his own voice begging it to stop. That when the moment arose, he would gladly accept his own death as a blessed gift. John knew that his father was tired. That he wished only for sleep, and to dream without waking. But he also knew that as long as the universe needed him, as long as there was something wrong that needed fixing, or someone needed help, the Doctor would come. Whenever a child cried, the Doctor would be there to help.

Sherlock brushed his thumb, the one from his real hand, along John's lip, eliciting a startled gasp from the man. "You were quiet, John. Is something wrong?"

"No. Not really. I was just thinking."

"About what?" Sherlock asked, curling further around John.

"Everything really. But mostly about how different it is." John murmured.

"You do like it though? You are happy?"

"Yes, I'm happy. I have you after all."

Sherlock grinned. "Good."

The two leant closer, lips millimetres apart. They were just about to kiss when a god-awful, ear-splitting racket began. The two pulled away, Sherlock clambering over John to pull on his robe and pyjama bottoms, John lying back for a moment and taking three deep breaths. Sherlock glanced at him, smirking. "You know, we can get back to this later. After we investigate the noise."

John chuckled, pulling himself up. When he was suitably dressed, the pair strolled into the control room to find the Doctor and a woman with very curly hair having a shouting match about how to correctly drive the TARDIS. Meanwhile, Amy was fighting Rory to be the first one to give River a bone-crushing hug, which was quickly becoming an all out brawl. "What the bloody hell is going on?" John shouted over the din.

There was an immediate lull in River and the Doctor's argument as the pair whirled to face him, and Rory paused long enough for Amy to break free from his arms and wrap her arms around River. River patted her mother on the head, beckoning to John with the other. "Oh, John. Look how much you've grown."

"Um, are you…?" John trailed off, looking uncertainly to the Doctor.

"Yes, John, it's me. I'm your mother." River said.

"You took the pocket watch from me… why didn't you ever come back? I thought you were dead." John asked quietly.

"I'm sorry, John. The Silence needed to think they had won. I couldn't let them get to you, I couldn't let them take you away. And... I always came back. I was always there, watching you grow up. You were my son, John, and I couldn't just let you go." River replied. River's eyes flicked towards Sherlock, running over him carefully. Her eyebrow arched as she turned back to John. "And who is this?"

"Oh, this is, ahem, Sherlock. He's my…" John trailed off awkwardly, unsure of what he and Sherlock were exactly to one another.

"He's John's special friend." The Doctor burst out, bustling over to the console. "Which reminds me, we have to go pick up Jack from wherever he is and find out what's wrong of the Planet of Maraken. I keep getting corroded messages over the psychic paper."

"Sounds interesting." River said, drawing John into a tight hug and whispering, "nice choice, my boy. He's a pretty one."


End file.
